I need to visually compare two documents of different formats, hence I would like to be able to vertically scroll in two different applications at the same time. I'd prefer to use the mouse wheel to do so. I know Notepad++ has a similar functionality.

Notepad++ has the ability to do sync'd vertical scrolling for plain text docs and source code - as do many other 'dev'-type document apps - but as slhck says it would help to know what you are currently using and what type of docs you are trying to view.

Edit: based on your useful feedback - here's a possible solution:

It's pretty straightforward to convert any doc to a PDF so if you get both docs in that format you can use something like DiffPDF to scroll through them both:

Thank you, i should have been more precise. See my comment on the original question. I was thinking of Notepad++ when I asked this, and would like to have the same functionality between two different applications.
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kowalskiAug 23 '11 at 9:25

Thanks for the references, I would +1 if I could ! In this case though, I cannot rely on a diff tool, the control can only be human made. I note your references for another task.
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kowalskiAug 23 '11 at 13:29